How do I automate extracting multiple gene sequences from multiple genomes?

omicR for R studio creates fasta files, downloads genomes from NCBI using the refseq number, creates databases to run BLAST+, runs BLAST+ and filters these results to obtain the best match per sequence. These scripts can be used to run BLAST alignment of short-read (DArTseq data) and long-read sequences (Illumina, PacBio… etc). You can use refer…

Automações para realizar alinhamentos em grande escala com o Blast

The impact of transitive annotation on the training of taxonomic classifiers

DNA barcoding analysis pipeline

A typesafe Scala BLAST API

Filter out sequences in FASTQ files that match a reference genome

The Blastn (Basic Local Alignment Search Tool for Nucleotides) algorithm with Smith-Waterman scoring implemented for FPGAs

This repository conatins bash scripts for performing a blast search using a custom database of BOLA-DRB3 alleles that were sequenced using Sanger sequencing.

BLAST without Sys.Call()

various tools that help with deep sequencing analysis

PhylUp - a python package to automatically generate alignments (or update alignments and phylogenies) using local sequences or a local Genbank database while controlling for the number of sequences per OTU.

BLAST searches in parallel using GNU Parallel

MIP_ORACLE: Identifies unique target regions with diagnostic significance in pathogens.

Scripts to run benchmarks of BLAST and PLAST on a supercomputer

Map SNP positions to a supplied reference assembly using BLAST. Filter results for best hit. Output in plink format.

A tool for analyzing transfers between genomes

A beginner’s guide to Bioinformatics

Parser of BLAST results